Abstract Embryonic stem cells (ESCs) exhibit two unique features that make them potential tools for the development of therapies for degenerative diseases. First, ESCs have the capacity to differentiate into any cell type, a property termed pluripotency. Second, ESCs have the ability to proliferate indefinitely in culture in an undifferentiated state without accumulating genetic or epigenetic alterations, a process called self- renewal. The decision of ESCs to self-renew or differentiate is ultimately controlled by several transcription factors called ESC master regulators, along with regulators of chromatin structure. In recent years, the gene targets and functions of the ESC master regulators have become better understood. In contrast, the targets and gene regulatory functions of most chromatin regulators required for ESC self-renewal or pluripotency are unknown. This project aims to understand the functions and mechanisms of action of three chromatin regulatory complexes with crucial functions in ESC self-renewal and pluripotency. The Tip60- p400 complex has lysine acetyltransferase (KAT) and nucleosome remodeling activities, and functions to silence differentiation-induced genes in self-renewing ESCs. This finding was unexpected, given the fact that most KATs function primarily in activation of transcription, and the documented roles of Tip60-p400 complex in gene-activation in somatic cells. We will examine the mechanism by which the Tip60-p400 complex silences differentiation genes in murine ESCs, and determine how this activity is regulated during differentiation. In addition, we recently found that two additional chromatin regulatory complexes, NURD and BAF, oppositely regulate an overlapping set of target genes, which are expressed at moderate levels as a result of this opposition. We will examine the mechanisms underlying this opposition, its importance in the maintenance of the pluripotent state, and its function in ESC differentiation.